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Golgi alpha-Mannosidase II in complex with 5-substituted swainsonine analog: (5R)-5-[2'-oxo-2'-(phenyl)ethyl]-swainsonine
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3BUB
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7 298 PEG8000, Tris, pH 7, 2.5% MPD, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.2 44.12
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 69.025 α = 90 b = 109.883 β = 90 c = 138.959 γ = 90
Symmetry Space Group P 21 21 21
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 CCD ADSC QUANTUM 4 2004-08-11 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON CHESS BEAMLINE F1 0.9186 CHESS F1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Net I Over Average Sigma (I) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot 1 1.32 30 97.7 0.072 15.3 5.04 247309 241556
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.32 1.34 87.5 0.276 4.46 3.21 5479
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 3BUB 1.32 29.22 247145 227621 5203 92.1 0.157 0.157 0.1553 0.182 0.1533 RANDOM 15.273
Temperature Factor Modeling Anisotropic B[1][1] Anisotropic B[1][2] Anisotropic B[1][3] Anisotropic B[2][2] Anisotropic B[2][3] Anisotropic B[3][3] -0.01 0.02 -0.02
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.659 r_dihedral_angle_4_deg 19.187 r_dihedral_angle_3_deg 12.083 r_dihedral_angle_1_deg 6.049 r_sphericity_free 5.058 r_sphericity_bonded 3.721 r_scangle_it 3.393 r_scbond_it 2.526 r_mcangle_it 1.793 r_rigid_bond_restr 1.747
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.659 r_dihedral_angle_4_deg 19.187 r_dihedral_angle_3_deg 12.083 r_dihedral_angle_1_deg 6.049 r_sphericity_free 5.058 r_sphericity_bonded 3.721 r_scangle_it 3.393 r_scbond_it 2.526 r_mcangle_it 1.793 r_rigid_bond_restr 1.747 r_angle_refined_deg 1.395 r_mcbond_it 1.235 r_nbtor_refined 0.308 r_nbd_refined 0.199 r_symmetry_vdw_refined 0.192 r_symmetry_hbond_refined 0.125 r_xyhbond_nbd_refined 0.119 r_chiral_restr 0.094 r_bond_refined_d 0.011 r_gen_planes_refined 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 8193 Nucleic Acid Atoms Solvent Atoms 1295 Heterogen Atoms 44
Software Software Software Name Purpose REFMAC refinement CNS refinement PDB_EXTRACT data extraction ADSC data collection HKL-2000 data reduction SADABS data scaling CNS phasing